Harms Lab @ University of Oregon
Software projects created by members of the the Harms lab at the University of Oregon
Eugene, OR
Pinned Repositories
epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
fast_dbscan
fast, lightweight dbscan implementation for peptide strings
gpmap
A Python API for managing genotype-phenotype map data
hops
Use machine learning to find rules for peptide binding
latticegpm
Python package for building fitness landscapes from protein lattice models
latticeproteins
2d protein lattice model simulator in Python
notebooks-nonlinear-high-order-epistasis
Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"
pdbtools
A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files
pytc
python program for analyzing isothermal titration calorimetry data
topiary
Python framework for doing ancestral sequence reconstruction
Harms Lab @ University of Oregon's Repositories
harmslab/epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
harmslab/topiary
Python framework for doing ancestral sequence reconstruction
harmslab/gpmap
A Python API for managing genotype-phenotype map data
harmslab/hops
Use machine learning to find rules for peptide binding
harmslab/fast_dbscan
fast, lightweight dbscan implementation for peptide strings
harmslab/gpseer
A tool to predict missing data in sparsely sampled genotype-phenotype maps
harmslab/dataprob
Library for fitting models using a likelihood framework.
harmslab/gpvolve
A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.
harmslab/flowsym
A Python API for simulating flow cytometry data.
harmslab/topiary-examples
Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package
harmslab/asr-protocol
Protocol and scripts for doing ancestral sequence reconstruction
harmslab/ellipticbn
tool for measuring ellipticity of cucurbituril macrocycles
harmslab/gpgraph
NetworkX for genotype-phenotype maps
harmslab/eee
ensemble epistasis engine
harmslab/ensemble_epistasis
harmslab/experimental-ensemble-epistasis
Scripts and data for reproducing the analysis in "An experimental demonstration of ensemble epistasis in the lac repressor"
harmslab/gelquant
Simple SDS-PAGE/western blot gel quantification software.
harmslab/gmx-template
template for setting up MD simulations in the Harms lab.
harmslab/hops_enrich
software for processing phage display data for machine learning with peplearn
harmslab/linkage
package for fitting thermodynamic linkage models to experimental data
harmslab/m63f-biophysics
scripts and data to reproduce biophysical investigation of S100A9/M63F
harmslab/riboswitch-epistasis
calculations and analysis files for riboswitch ensemble epistasis manuscript
harmslab/rosetta-docking
scripts for doing rosetta docking calculations
harmslab/setup_md
Files and scripts used to set up MD simulations in the Harms Lab
harmslab/stability-constraint-ms-figures
code to generate figures and do analyses for hS100A9/M63F stability constraint study
harmslab/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
harmslab/venninator
estimate overlaps between sets
harmslab/vertebrate-tlr4-evolution
scripts for reproducing vertebrate tlr4 synteny analysis
harmslab/website
Website for the lab
harmslab/were-anc-less-specific
notebooks and scripts to reproduce analyses from "Were Ancestral Proteins Less Specific" manuscript